Learn R Programming

RADami (version 1.1-2)

Phylogenetic Analysis of RADseq Data

Description

Implements import, export, manipulation, visualization, and downstream (post-clustering) analysis of RADseq data, integrating with the 'pyRAD' package by Deren Eaton.

Copy Link

Version

Install

install.packages('RADami')

Monthly Downloads

7

Version

1.1-2

License

GPL-3

Maintainer

Andrew Hipp

Last Published

February 11th, 2017

Functions in RADami (1.1-2)

genotypes.pyRAD.loci

Generates genotypes from a
gen.RAD.loci.datasets

Generate datasets for partitioned RAD analysis
consensus.pyRAD

Generate a consensus sequence for each of the loci in a pyRAD.loci object
filter.by

Identify names of loci for which at the requested taxa are present,
get.raxml.siteLikelihoods

lengths.report

Return the lengths of all loci in a pyRAD.loci object
genTrees

compare.all.trees

Compare all trees in a treeset, and return a matrix (lower diagonal only) indicating which pairwise comparisons are identical
grab.pyRAD.locus

Extract sequence data for one or a few loci
get.raxml.treeLikelihoods

Extract likelihoods from a RAxML info file
pairwise.fst.loci

Returns pairwise FST list for groups of individuals
locus.dist

Generate a pairwise similarity matrix for individuals based on locus-sharing patterns
print.pyRAD.loci

Print method for
plot.rankedPartitionedRAD

Plot a
plot.locus.dist

Plot a phylogeny with a graphical representation of locus sharing
oak.tree

28-tip oak phylogeny, in
oak.rads

101-locus RAD dataset, in
overlap.report

Generates a report on locus overlap between pairs of samples named in a structured fashion
match.lnL.to.trees

Match the likelihoods returned on a subset of trees for numerous loci to the trees originally input
plot.partitionedRAD

Plot a
rad2mat

Generates a matrix of sequences from a
summary.pyRAD.loci

Summary method for
tidyName

write.DNAStringSet

Writes a sequence matrix to phylip format
rad2phy

Export a
RADami-package

Phylogenetic Analysis of RADseq Data
subset.pyRAD.loci

Subsets a
rank.partitionedRAD

Bin trees into 'suppported' or 'disfavored' by locus.
rtreePhylo

Generate random trees using an input tree to get taxon names and tips
read.pyRAD

Read in data from pyRAD